Module 1 - Structure and Bonding and Reaction Mechanisms

CHEM 40: Basic Organic Chemistry
Module 1: Bonding, Structure, and Reaction Mechanisms
This material has been reproduced and communicated to you by or on behalf of University
of the Philippines pursuant to PART IV: The Law on Copyright of Republic Act (RA) 8293 or the
“Intellectual Property Code of the Philippines.”
The University does not authorize you to reproduce or communicate this material. This
material may contain works that are subject to copyright protection under RA 8293. Any
reproduction and/or communication of the material by you may be subject to copyright
infringement and the copyright owners have the right to take legal action against such
infringement.
Do not remove this notice.
MODULE 1. BONDING, STRUCTURE, AND REACTION MECHANISMS
Introduction
As a science, organic chemistry is less than 2000 years old. As we know it today, organic
chemistry had its beginning in the latter part of the 18th century. Substances were classified into
inorganic, from the mineral world such as salts, metals, rocks, and glass; and organic, from animal
and vegetable sources (any materials produced by living organisms. Jöns Jacob Berzelius in 1807
coined the term organic chemistry for the study of compounds derived from natural sources.
Today, organic compounds are key components of plastics, soaps, perfumes, sweeteners, fabrics,
pharmaceuticals, and many other substances that we use every day. The value to us of organic
compounds ensures that organic chemistry is an important discipline within the general field of
chemistry.
Objectives
At the end of this module, the students should be able to:
● appreciate the origins, nature and scope of organic chemistry;

● differentiate the bonding theories;
● differentiate ionic and covalent bond;
● write correct Lewis structures;
● determine hybridization of carbon atoms and geometry of molecules;
● identify bonds as sigma or pi;
● recognize functional groups and classes;
● identify types of reactions, reagents, bond cleavage and formation, and intermediates;
● identify reaction mechanisms as homolytic or heterolytic; and
● interpret reaction energy diagrams with respect to kinetic and thermodynamic aspects,
number of steps, and rate limiting step.
1
This module is intended only for your personal use in connection with the course you are enrolled in. It
is not for distribution or sale. Permission should be obtained from the Organic Chemistry and Natural
Products Division for any use other than for what it is intended.
1.1. Highlights- History of Organic Chemistry
The practice of organic chemistry dates back since prehistoric time. Ancient Egyptians
used organic compounds such as indigo and alizarin to dye clothes. In India, as early as 2500 BC,
indigo was used to dye cloth a deep blue. Ancient Phoenicians used Tyrian purple from mollusks
to dye cloth a deep purple. Fermentation of grapes to produce ethyl alcohol and the acidic
qualities of sourced wine are both described in the bible and were probably known earlier. Early
Chinese civilizations (2500 to 3000 BC) extensively used natural materials for treating illnesses.
According to the theory of vital force, compounds derived from natural sources (organic) were
fundamentally different from inorganic compounds. One consequence of this theory, chemists
believed, was that organic compounds could not be prepared and manipulated in the laboratory
as could inorganic compounds.
As early as 1816, however, this vitalistic theory received a heavy blow when Michel
Chevreul found that soap, prepared by the reaction of alkali with animal fat, could be separated
into several pure organic compounds, which he termed fatty acids. For the first time, one organic
substance (fat) was converted into others (fatty acids plus glycerin) without the intervention of
an outside vital force. The German chemist Friedrich Wöhler was one of the early chemists to
refute vitalism. In 1828, he reported the synthesis of urea, a component of many body fluids,
from nonliving materials.
This scientific milestone is the first organic synthesis and demonstration of isomerism,
which is the phenomenon in which more than one compounds have the same chemical formula
but different chemical structures. In 1845, Kolbe coined the term synthesis and contributed to
the philosophical demise of vitalism through synthesis of the organic substance acetic acid from
carbon disulfide. Berthelot then synthesized methane (contaminated with a little ethylene) by
passing a mixture of carbon disulfide vapor and hydrogen sulfide over red-hotcopper. Then in
1857, by reacting methane with chlorine, he obtained methyl chloride, which, on hydrolysis,
formed methyl alcohol. Since then, it has been recognized that organic molecules obey the same
natural laws as inorganic substances, and the category of organic compounds has evolved to
include both natural and synthetic compounds that contain carbon.
2
1.2. Bonding and Structure
1.2.1. The Nature of Organic Compounds
Have you ever wondered why there are millions of organic compounds, which is far more
than the number of inorganic compounds? The reason lies in the fact that carbon has unique
ability that sets it apart from all other elements in the periodic table. But why is carbon special?
August Kekulé (Germany) and Couper (Scotland) were the first to recognize in 1858 that
carbon is tetravalent- it can form four bonds, not only with other atoms (mainly H, O, N) but
also with other carbon atoms. The most distinctive feature of carbon atoms is their capacity to
form very strong covalent bonds with each other. No other element, including silicon, can do this.
Silicon-silicon bonds are easily cleaved. Silicon-oxygen-silicon bonds are quite strong but do not
result in the incredible diversity found in carbon compounds. Carbon is able to form an immense
diversity of compounds, from the simple to the staggeringly complex. It can link with each other
to form linear, branched or cyclic backbones for a wide variety of organic molecules. Take for
example only four carbon atoms and see the number of ways by which they can be linked to one
another.
You can just imagine how many diverse molecular frameworks can result if there are more
carbon atoms that are being linked to one another! Moreover, carbon atoms may participate in
single, double or triple bonds.
In general, organic compounds, which are largely covalent compounds, have low melting
points and limited solubility in water. Some are gases, and many are liquids in room temperature;
those that are solid melts below 400 °C. In contrast many inorganic salts, which are ionic
compounds, melt above 1000 °C and dissolve readily in water. Organic compounds are generally
combustible (flammable) and/or are sensitive to heat (decomposed by heat).
Organic chemistry is an empirical science whose developments have depended on millions

of separate laboratory observations. These observations have been rationalized and unified by
3
structural theory. This theory uses a few simple ideas to account for diverse complex phenomena
and to allow predictions to be made about millions of compounds that have never been but might
be known. With the structural theory as a guide, many organic chemists have designed and
synthesized hundreds of new organic compounds during their lifetimes.
Fundamental to the structural theory are two central premises:
1. Atoms in organic molecules from a fixed number of bonds; the measure of this ability is
called valence. For example, carbon forms four bonds and is called tetravalent.
2. A carbon atom uses one or more of its valences to form bonds to other carbon atoms, i.e.
carbon can participate in single, double and triple bonds.
1.2.2. Electronic Structure and Bonding
The electrons in the outermost shell are the ones involved in the formation of chemical
bonds and in chemical reactions. These electrons are called valence electrons, and the energy
level in which they are found is called the valence shell. To show the outermost shell electrons
of an atom, a representation called a Lewis structure is used. In Lewis structures, the atomic
symbol represents the nucleus and all the completely inner shells. The symbol is surrounded by
a number of dots equal to the number of valence electrons.
1.3. The Formation of Chemical Bonds
Gilbert N. Lewis pointed out that the chemical inertness of the noble gases indicated a
high degree of stability of the electron configuration of these elements (the noble gases have
completely filled valence shells). Lewis then devised a model of bonding that unified many of the
observations about chemical reactions of the elements. According to the Lewis scheme, atoms
bond together in such a way that each atom participating in a chemical bond acquires a completed
valence shell electronic configuration resembling that of a noble gas nearest it in the periodic
table. The force that holds atoms together in a molecule or crystalline lattice is referred to as a
chemical bond.
There are two ways by which atoms acquire completely filled valence shells:
1. gaining or losing enough electrons- an atom that gains an electron becomes a

negatively charged ion; on the other hand, an atom that loses electrons becomes a
positively charged ion; the chemical bond between positively charged and negatively
charged ions is called an ionic bond.
2. Sharing of electrons with other atoms or atoms- the chemical bond formed is called
covalent bond.
4
1.3.1. The Ionic Bond
An ionic bond is formed by the transfer of electrons from one atom to another. Atoms
having low ionization energy loses electrons easily. Ionization energy is the amount of energy
required to remove the most loosely held electron from an isolated atom in its ground state.
The alkali metals found at the far left of the periodic table have low ionization energy and
so give up electrons easily. Across the periodic table, from left to right, there is a general increase
in the ionization energy of the representative elements.
Atoms that have high electron affinity (EA) gain electrons easily. Electron affinity is the
amount of energy released when an electron is added in its ground state.
In general, electron affinity of representative elements increases in going from left to right
of the periodic table. The halogens which appear at the right side of the periodic table have high
electron affinity and so gain electrons easily. Ionic compounds contain charged particles held
together by extremely strong electrostatic interactions. For example, sodium chloride is formed
through ionic bonding between sodium and chlorine.
Sodium has low ionization potential and so readily loses one electron to form Na+ which
has electron configuration of the noble gas neon. Chlorine has high affinity and readily gains one
electron.
1.3.2. The Covalent Bond
Atoms in the middle of the periodic table require too much energy to gain or lose sufficient
electrons in order to attain the electron configuration of the noble gases.
● these atoms acquire completely filled valence shells by sharing electrons

● an atom forms as many covalent compounds with other atoms as the number of
electrons to fill the valence shell.
5
A covalent bond is formed by sharing of electrons by two atoms. The formation of

hydrogen molecules is the simplest example of the formation of a covalent bond. When two
hydrogens combine, the electron from one atom combines with the electron of the other to form
an electron pair. The shared electrons now belong to both hydrogen atoms. Each of the two
atoms in a covalent bond used the two electrons in the bonds to acquire a noble gas electron
configuration. Thus, each hydrogen atom in the hydrogen molecule acquires the electron
configuration of the noble gas helium. Covalent compounds have structural units called molecules.
A molecule is a neutral collection of atoms held together by covalent bonds.
Examples:
In Lewis structures, a covalent bond is indicated by a pair of dots that lie between the two
bonded atoms. As a shorthand notation, a pair of electrons in a covalent bond is shown as a dash
or a short line between the bonded atoms; an unshared electron pair (lone pair) is shown as a
pair of dots. Let us now rewrite the structures of methane, ammonia and water using the line
and lone-pair notation.
An atom can form as many covalent bonds with other atoms as the maximum number of
electrons needed to fill its valence shell.
6
Hydrogen with one valence electron needs one electron to fill its valence shell and
therefore can form one covalent bond. Carbon with four valence electrons, needs four more to
fill its valence shell and therefore forms four covalent bonds.
By similar reasoning, nitrogen with five valence electrons forms three covalent bonds;
oxygen with six valence electrons forms two covalent bonds; and the halogens (F, Cl, Br, I) with
seven valence electrons form one covalent bond.
Below are some examples which illustrate these different bonding capacities.
Carbon, nitrogen, and oxygen can form more than one bond between pair of atoms.
Sharing of one electron pair leads to a single bond. Sharing of two electron pairs leads to a double
bond, while sharing of three electron pairs leads to a triple bond. The sharing of four electron
pairs is not observed.
1.4. Writing Correct Lewis Structures
Lewis structures are used as a simple, shorthand and convenient notation for
representing the electronic structures of atoms, ions and molecules, which provide an accurate
accounting of electrons. Facility with writing correct Lewis structures is important in the study of
organic chemistry.
There are two necessary features for a correct Lewis structure:
1) the electrons in the valence shell of each atom are assigned correctly, and
2) the formal charges are assigned correctly.
Sometimes covalently bonded atoms have a charge; this is called formal charge. The charge
of an atom depends on the number of electrons available to it and the number of protons in its
nucleus. To determine the number of electrons in the valence shell of an atom, we count all the
electrons of covalent bonds plus any shared electrons. To assign formal charge to an atom, we
count half of the shared plus any unshared electrons and subtract their number from the number
of valence electrons in the neutral, unbonded atom.
7
We can make certain generalizations about the structures of the uncharged molecules we
have encountered so far:
1) A carbon with four covalent bonds is neutral.

2) A nitrogen atom with three covalent bonds and one electron pair is neutral.
3) Halogens (F, Cl, Br, I) with one covalent bond and three lone pairs are neutral.
In the following exercises you will encounter examples where atoms have formal charges.
So far, we have considered the Lewis model of bonding which describes chemical bonds in terms
of the valence electrons.
SAQ 1-1. Lewis Structure
Write a Lewis structure for each of the following:

1. CH3F 7. NH4OH
2. CH3CH3 8. H3O+
3. H3PO4 9. NH4+
4. H2CO3 10. NaOH
5. HNO3 11. CH2O
6. H2SO4 12. CH3OCH3
Resonance structures are a set of two or more Lewis Structures that collectively
describe the electronic bonding of a single polyatomic species including fractional bonds and
fractional charges. Resonance structures are capable of describing delocalized electrons that
cannot be expressed by a single Lewis formula with an integer number of covalent bonds.
8
Example:
Recommended Online Reading
If you would like to learn more how to draw Lewis structures properly, click the following
hyperlinked texts.
1) Lewis Symbols and Structures

2) Formal Charges: Mathematical and Intuitive Method
3) Formal Charges and Resonance
1.5. Writing Molecular and Structural Formula
The structures of organic molecules may also be represented in a less detailed manner by
condensed formulas. Instead of the usual format for chemical formulas in which each element
symbol appears just once, a condensed formula is written to suggest the bonding in the molecule.
These formulas have the appearance of a Lewis structure from which most or all of the bond
symbols have been removed.
9
Example:
Lewis structures and ball-and-stick models of methane, ethane, and pentane.
A common method to simplify the drawings of larger molecules is to use a skeletal

structure (also called a line-angle structure). In this type of structure, carbon atoms are not
symbolized with a C, but represented by each end of a line or bend in a line. Hydrogen atoms are
not drawn if they are attached to a carbon. Other atoms besides carbon and hydrogen are
represented by their elemental symbols. The figure below shows three different ways to draw the
same structure.
The same structure is represented in three different ways: an expanded formula, a condensed
formula, and a skeletal structure (or shorthand formula).
10
SAQ 1-2. Drawing Skeletal Structures
Draw the skeletal structures for these two molecules:
Condensed formula Skeletal structure
1.
2.
3.
4.
5.
1.6. Isomers
Organic molecules exhibit isomerism, a term derived from the Latin iso (equal) and mer
(part). There are two general types of isomerism: structural isomerism and
stereoisomerism. Structural isomers (also known as constitutional isomers) have the same
molecular formula but different structural formulas, i.e., the same atoms can be put together in
different ways resulting in different compounds with entirely different properties. As the number
of carbon increases, the number of possible structures corresponding to a molecular formula also
increases.
For example, two structural formulas can be derived from the molecular formula C2H6O,
and each one corresponds to a different compound.
11
Constitutional isomers are different compounds that have the same molecular formula but
differ in the sequence in which their atoms are bonded, that is, in their connectivity. These isomers
usually have different physical properties (e.g., melting point, boiling point, and density) and
different chemical properties (reactivity). For instance, ethyl alcohol and dimethyl ether are
constitutional isomers and these compounds have different boiling point.
The three classification of constitutional isomers are the following:

1. Skeletal isomers
2. Functional group isomers
3. Positional isomers
Click each hyperlinked text and read the online resources to understand the different types of
constitutional isomers.
SAQ 1-3. Constitutional Isomers

Consider each pair of structural formulas that follow and state whether the two formulas
represent the same compound, whether they represent different compounds that are
constitutional isomers of each other, or whether they represent different compounds that are
not isomeric.
12
1.7. Index of Hydrogen Deficiency (IHD)
In a hydrocarbon where all the C atoms have only single bonds and no rings are involved,
the compound would have the maximum number of H atoms. If any of the bonds are replaced
with double or triple bonds, or if rings are involved, there would be a “deficiency” of H atoms. By
calculating the index of hydrogen deficiency (IHD), we can tell from the molecular formula
whether and how many multiple bonds and rings are involved. IHD is also called the Degree of
Unsaturation, signified by the symbol “”. This will help cut down the possibilities one has to
consider in trying to come up with all the isomers of a given formula.
Here is a summary of how the index of hydrogen deficiency (IHD) works.
● A double bond and ring each count as one IHD.
● A triple bond counts as two IHD.
● Keep in mind the value of IHD should be an integer.
Example: Write the possible structural formulas for:

a) C2H6O
b) C3H6
Answer:
2+(2∗2)−6
a) 𝐼𝐻𝐷 = 2
= 0, an IHD value of 0 indicates that there is no double bond, triple
bond or ring
Hence, the structural formula of C2H6O is
or
2+(2∗3)−6
b) 𝐼𝐻𝐷 = 2
= 1, an IHD value of 0 indicates that there is 1 double bond
or 1 ring
13
The structural formula of C3H6 is:
or
SAQ 1-4. Index of Hydrogen Deficiency
Consider the molecular formula C3H6O, write all the possible structural formulas. Hint: You can
calculate IHD to determine the number of multiple bonds and rings that could be possibly
present in the compounds.
1.8. CHEMICAL BONDING THEORIES
How does electron sharing occur? Before we proceed in the discussion of theories that
describe bond formation, let us review the fundamental concepts of electron configuration from
your general chemistry course.
Rule 1 The lowest-energy orbitals fill up first, according to the order 1s 2s 2p 3s 3p 4s

3d, a statement called the Aufbau principle. Note that the 4s orbital lies
between the 3p and 3d orbitals in energy.
Aufbau principle describes the rules for determining the electron
configuration of an atom.
Rule 2 Electrons act as if they were spinning around an axis, in much the same way
that the earth spins. This spin can have two orientations, denoted as up ↑ and
down ↓. Only two electrons can occupy an orbital, and they must be of opposite
spin, a statement called the Pauli exclusion principle.
Pauli exclusion principle states that no more than two electrons can occupy
the same orbital, and those two electrons must have spins of opposite sign.
Rule 3 Hund’s rule states that if two or more empty orbitals of equal energy are
available, one electron occupies each, with their spins parallel, until all are
half-full.
SAQ 1-5. Electron Configuration

Give the ground-state electron configuration for each of the following elements:
(a) Oxygen
(b) Silicon
(c) Sulfur
14
1.8.1. VALENCE BOND THEORY (VBT)
According to VBT, a covalent bond results when two atoms approach each other closely
so that a singly occupied orbital on one atom overlaps a singly occupied orbital on the other atom.
The electrons are now paired in the overlapping orbitals and are attracted to the nuclei of both
atoms, thus bonding the atoms together. Here are the key ideas of VBT:
● Covalent bonds are formed by overlap of two atomic orbitals, each of which contains one
electron. The spins of the two electrons are opposite.
● Each of the bonded atoms retains its own atomic orbitals, but the electron pair in the
overlapping orbitals is shared by both atoms.
● The greater the amount of orbital overlap, the stronger the bond.
In the H2 molecule, for example, the H—H bond results from the overlap of two singly
occupied hydrogen 1s orbitals. In this figure, the overlapping orbitals of the H2 molecule form an
elongated egg shape. If we are going to pass a plane right at the middle of the bond, we’ll get
a circle, implying that the bond is cylindrically symmetrical. Such bonds are formed by a head-
on overlap of two atomic orbitals along the line drawn between the two nuclei, giving rise to a
sigma bond.
During the bond-forming reaction (see the illustration below), 436 kJ/mol of energy is
released. Because the product H2 molecule has 436 kJ/mol less energy than the starting 2 H·
atoms, we say that the product is more stable than the reactant and that the H-H bond has a
bond strength of 436 kJ/mol. In other words, we would have to put 436 kJ/mol of energy into
the H-H bond to break the H2 molecule apart into H atoms.
15
How close are the two nuclei in the H2 molecule? If they are too close, they will repel each
other because both are positively charged, yet if they’re too far apart, they won’t be able to share
the bonding electrons. Thus, there is an optimum distance between nuclei that leads to maximum
stability referred to as bond length. Below is a plot of energy versus internuclear distance for two
hydrogen atoms. The distance between nuclei at the minimum energy point is the bond length.
1.8.2. Summary: Properties of Covalent Bond

In summary, the properties of a covalent bond are:
1. Bond strength is an alternative name for bond dissociation energy, which is the amount
of energy needed to break a bond homolytically and produce two radical fragments. It
also refers to the amount of energy consumed when a bond is broken is equal to the
amount of energy liberated when a bond is formed.
2. Bond length is the equilibrium distance between the nuclei of two atoms that are
bonded to each other.
Important!
Watch the short discussion “Bond Strength and Length” to understand the relationship of these
two properties. Click the hyperlinked text.
3. Bond angle is the angle formed between two adjacent bonds.
4. Bond polarity is a measure of the distribution of electrons between two bonded atoms.
o Polar bond- joins atoms of different electronegativity
o Nonpolar bond- joins atoms of equal electronegativity
o Electronegativity:
F > O > Cl, N > Br > C, H
16
1.8.3. MOLECULAR ORBITAL THEORY (MOT)

MOT describes covalent bond formation as arising from a mathematical combination of
atomic orbitals to form molecular orbitals.
● # MOs = #AOs combining
A molecular orbital (MO) describes a region of space in a molecule where electrons are
most likely to be found. Like in an atomic orbital (AO), a molecular orbital has its own shape,
size and energy.
Here are the key ideas of MOT:

● molecular orbitals are to molecules what atomic orbitals are to atoms
● molecular orbitals are formed by combining atomic orbitals
o the number of molecular orbitals formed is equal to the number of atomic
orbitals combined
● relative energies of molecular orbitals:
o bonding MO (lower energy than AO)
o nonbonding MO (same energy as AO)
o antibonding (higher energy than AO)
Consider F2 as an example, there are two possible orbital overlaps, which may be:
1.9. Hybridization
Hybridization is the idea that atomic orbitals fuse to form newly hybridized orbitals, which in
turn, influences molecular geometry and bonding properties. Hybridization is also an expansion
of the valence bond theory. In order to explore this idea further, we will utilize three types of
hydrocarbon compounds to illustrate sp, sp2, and sp3 hybridization.
Type of hybrid No. of s No. of p No. of p No. of hybrid

orbital participating participating remaining orbitals formed
sp 1 1 2 2
sp2 1 2 1 3
sp3 1 3 0 4
We will utilize three types of hydrocarbon compounds to illustrate sp3, sp2, and sp
hybridization.
17
1.9.1. sp3 hybridization, methane as an example
First and foremost, it is important to note that carbon has the electron configuration of
1s2 2s2 2p2. This means that carbon would have 2 unpaired electrons in its p orbitals. Theoretically,
this means that carbon will only form 2 bonds, but that is definitely not the case.
As seen in methane (CH4), carbon can form 4 bonds. Supporting evidence shows that 1 s
and 3 p orbitals are being combined to form hybrid orbitals, allowing polyatomic molecules to
have 25% s character and 75% p character. Thus, we call methane a sp3-hybridized molecule.
There are 4 hybridized orbitals orienting as far away from each other as possible. Thus,
hybridization explains why there is a 109° angle between orbitals.
18
1.9.2. sp2 hybridization, ethylene as an example
Unlike methane, ethylene is shaped differently, despite the fact that the carbon in ethylene
has the same electron configuration. What accounts for this difference? Supporting evidence
shows that the carbon in an ethylene molecule is sp2 hybridized. This means that 1 s orbital is
being mixed with 2 p orbitals.
This time, the energy diagram setup is different because only 2 p orbitals are being mixed.
By placing two electrons in the same orbital, Hund's rule was broken, which states that all orbitals
among the same energy levels have to be filled with at least one electron before being paired up
again. The 2p orbital here is considered low enough energy to be classified within the same
energy level as the sp2 orbitals. The figure below portrays the correct way to distribute your
electrons.
Notice how that lone electron in the 2p orbital is separate from the electrons in the sp2
orbitals. This is what influences ethylene's shape. The lone electron from each carbon will remain
in its respective p orbital and form a pi bond with the other p orbital electron. Thus, ethylene is
a planar molecule, with orbitals spaced 120° angles apart.
19
The hot pink sp2 hybridized orbitals are all on the same plane (let's say among the xy plane),
whereas the pi bonds are running along in a plane perpendicular to the xy plane. The figure above
accurately depicts the ethylene Lewis structure: The double bond in the Lewis structure is
indicative of one sigma bond and one pi bond.
1.9.3. sp hybridization, acetylene as an example
Supporting evidence shows that acetylene is a sp molecule. This means that 1 s orbital
is being mixed with 1 p orbital. Thus, the energy diagram setup would look like this:
As previously discussed, the lone electrons in the 2p orbitals are not part of the sp orbitals.
Instead, each electron is in its respective p orbital, and will bond with its respective p orbital of
the other carbon. This in itself will create a sigma bond and two pi bonds, leading to the formation
of a linear molecule.
Thus, in a Lewis structure, acetylene is composed of 2 triple-bond carbons: the bond

angle is 180 degrees, indicative of a linear molecule.
20
1.9.4. Examples of Overlapping Orbitals
21
1.9.5. Summary: Hybridization
Hybridization Summary
sp3
Case 1: methane, CH4
22
sp2
23
sp
24
Hybridization Generalization
sp3 Atoms of second row elements with 4 attached groups (i.e., lone pairs or
atoms) are usually sp3-hybridized.
Examples:
sp2 Atoms of second row elements with 3 attached groups are usually sp2-
hybridized.
Examples:
sp Atoms of second row elements with 2 attached groups are usually sp-
hybridized.
Examples:
25
Recommended Online Learning
To learn more about hybridization, read the following online resources by clicking the
hyperlinked texts.
1. Hybridization of Nitrogen, Oxygen, Phosphorus and Sulfur

2. Hybrid Atomic Orbitals
3. Atomic and Molecular Orbitals
SAQ 1-6. Hybridization
1. Determine the hybridization and the bond angle around atoms 1, 2, 3, and 4.
2. Arrange bonds A, B, and D according to:

a) Increasing bond length
b) Increasing bond strength
1.11. Classification of Organic Compounds
1.11.1. Classes of Organic Compounds
Organic compounds can be classified into two big groups- the hydrocarbons and those
with heteroatoms. The hydrocarbons are organic compounds containing only hydrogen and
carbon. Elements other than carbon and hydrogen found in organic compounds are called
heteroatoms. Among the most common heteroatoms are oxygen, nitrogen and halogens (Cl,
Br, F and I). In addition, sulfur and phosphorus are also found in several organic compounds.
26
Figure 1.1. The different classes of organic compounds
1.11.2. FUNCTIONAL GROUPS
The basis for classifying organic compounds into classes (or families) is structure. With
exception of alkanes, each class contains at least one functional group. The functional group
is the group of atoms that defines the structure and at the same time determines the properties
of a class or family of organic compounds. This means that compounds in the same class have
physical and chemical properties which are quite similar.
27
28
29
SAQ 1-7. Functional Groups
1. Encircle the functional group in the following compounds, label each with the letters
indicated and identify the class of compounds in which the functional group may be
found.
Chlorothalonil, a fungicide Functional group Class
A
B
C
Eugenol, component of clove oil
D
E
F
2. Identify the functional groups present in vindoline, an anti-cancer drug from periwinkle.
A ____________________
B ____________________
C ____________________
D ____________________
E ____________________
F ____________________
3. Write a structure for a compound of molecular formula C5H10O that contains the
indicated functional groups.
a) a carbon-carbon double bond and an alcohol
b) a ketone
c) an aldehyde
d) a carbon-carbon double bond and an ether
30
1.12. Introduction to Reaction Mechanisms
A. Types of Organic Reactions
I. Addition- there is an increase in the number of atoms/groups attached to carbon and is

usually accompanied by change in hybridization (increase in p character).
o the two reactants add together to form a single new product with “no atoms left-
over”
Example:
II. Elimination- there is a decrease in the number of atoms/groups attached to carbon and
is usually accompanied by change in hybridization (increase in s character).
o the opposite of addition; a single reactant splits apart into two products.
Example:
III. Rearrangement- there is a migration of an atom/group from one atom to another.
o a single reactant undergoes a reorganization of bonds and atoms to yield a

single isomeric product
31
Example:
IV. Substitution involves the replacement of an atom/group in the substrate by another

atom/group.
o two reactants exchange parts to form two new products
Example:
V. Oxidation- There is an increase in the oxygen and/or decrease in the hydrogen content
of the substrate.
32
Example:
VI. Reduction- There is an increase in the hydrogen content and/or a decrease in the oxygen
content of the substrate.
Example:
33
SAQ 1-8. Types of Organic Reactions.
Identify each type of reaction as addition, elimination, substitution, rearrangement, oxidation

or reduction.
34
1.12.2. Reaction energy diagrams
Energy is liberated when atoms combine to form molecules. When a molecule breaks up
into atoms, an equivalent amount is consumed. The amount of energy consumed or
liberated when a bond is broken or formed is referred to as dissociation energy, which is
a characteristic of a particular bond.
The energy changes that take place during a reaction are clearly described in the energy
diagram of the reaction, where we plot the potential energy of the reacting particles (y-
axis) against the reaction coordinate (x-axis). The energy diagram for a one-step
(concerted) hypothetical reaction is shown below:
35
A reaction that proceeds with a negative energy change (releases energy to its
surroundings) is said to be exergonic. Because the energy change is negative, we can say that
in energy terms the reaction goes downhill. The products of the reaction are at a lower level of
free energy than the reactants. In the example, a covalent bond is broken, thus, the reactants
must go up an energy hill first before they can go downhill.
● The reaction coordinate indicates the progress of the reaction, in terms of the conversion of
reactants to products.
● The top of the energy curve corresponds to the transition state (T.S) for the reaction.
● The activation energy for the reaction is the difference in energy between the reactants
and the transition state.
● The ∆H is the change in enthalpy of the system in the reaction or the difference in energy
between the reactants and the products.
● In the previous example, the energy level of the products is lower than that of the reactants.
In terms of our analogy, we can say that the reactants in one energy valley must surmount
an energy hill (the transition state) in order to reach the lower energy valley of the products.
If a reaction in which covalent bonds are broken proceeds with a positive energy change,
there will still be a free energy of activation. That is, if the products have greater energy than
reactants, the energy of activation will be even higher. In other words, in the uphill (endergonic)
reaction an even larger energy hill lies between the reactants in one valley and the products in a
higher one. The reaction that proceeds with a positive energy change (absorbs energy from its
surroundings) is said to be endergonic.
36
37
For a hypothetical two-step reaction, the energy diagram is shown below:
Example:
Free-energy diagram for the addition of HX to an alkene. The free energy of activation for step
1 is much larger than that for step 2.
38
The important step—because it is the rate-determining step—is step 1. This step is

highly endergonic and has a high free energy of activation. Consequently, it takes place slowly.
In step 2 the highly reactive carbocation stabilizes itself by combining with a halide ion. This
exergonic step has a very low free energy of activation and takes place very rapidly.
Consider the reaction:
There are many possibilities for this reaction, which can be illustrated in the following
energy diagrams:
39
1.12.3. Types of Bond Cleavage
Fundamentally, there are only two ways by which a covalent bond can break or cleave:
1. homolytic bond cleavage- the bond breaks in a symmetrical way such that each of the
atom joined by the bond gets one electron, resulting in fragments called free radicals; by
convention, a half-headed arrow designates the movement of a single electron and is
therefore used to indicate hemolytic cleavage.
Example:
2. heterolytic bond cleavage- the bond breaks in such a way that both electrons remain
with one atom, oftentimes resulting in the formation of positive and negative ions; a full-
headed arrow is used to designate movement of the electron pair
40
Example:
The formation of covalent bonds can occur through exactly the reverse of the
process above.
Example:
1.12.4. Types of Reagents
The reagent, together with the reaction conditions employed, determines the type of
bond cleavage that will occur in a reaction. There are three main types of reagents:
1. Electrophilic (electrophile)- electron-loving; usually Lewis acids

-species that are electron-deficient, and are capable of forming new bonds by accepting
a pair of electrons; they attack positions of high electron density
2. Nucleophilic (nucleophile)- nucleus-loving; usually Lewis bases

-species that have pairs of electrons that can be used in bond formation; they attack
positions with positive charge or low electron density
3. Radical-like- species that have an odd number of electrons; they are very reactive,
and their tendency is to pair up the single electron
Heterolytic bond cleavage occurs when an electrophilic or nucleophilic reagent attacks

a substrate. The reaction is called electrophilic or nucleophilic reaction.
41
Example:
On the other hand, homolytic bond cleavage occurs when a radical-like reagent attacks
a substrate. The reaction is called free-radical reaction.
Example:
methyl free radical
Suggested Online Resource:
Before you answer the following questions, read the online resource entitled “Everything
You Need to Know about Mechanisms”.
42
SAQ 1-9. Introduction to Reaction Mechanisms
I. Draw the necessary arrows.

Example:
II. Identify each reagent as nucleophile, electrophile, or free-radical.

III. Classify each bond cleavage as homolytic or heterolytic.
43
Recommended Online Resources
1. Click the following link and watch the lecture video that discusses valence bond theory.
https://ocw.mit.edu/courses/chemistry/5-111sc-principles-of-chemical-science-fall-2014/unit-ii-
chemical-bonding-structure/lecture-14/
2. Read the online resource entitled “Drawing Organic Structures” by clicking the following
hyperlinked text to learn more about writing formulas in different forms.
3. Go through the module by clicking the following to study how to write structural formulas
in different forms.
Structural Formulas - Lewis, Kekule, Bond-line, Condensed, & Perspective
References:
McMurry,S. & McMurry, J. (2011). Fundamentals of organic chemistry, seventh edition, John
McMurry /Belmont, CA: Brooks/Cole.
Morrison, R. T., & Boyd, R. N. (1983). Organic chemistry. Boston: Allyn and Bacon.
Solomons, T. W. G., & Fryhle, C. B. (2008). Organic chemistry. Hoboken, NJ: John Wiley.
44

Module 1 - Structure and Bonding and Reaction Mechanisms

Uploaded by

Document Information

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Module 1 - Structure and Bonding and Reaction Mechanisms

Uploaded by

Copyright:

Available Formats

CHEM 40: Basic Organic Chemistry

Module 1: Bonding, Structure, and Reaction Mechanisms

Do not remove this notice.

MODULE 1. BONDING, STRUCTURE, AND REACTION MECHANISMS

At the end of this module, the students should be able to:

● appreciate the origins, nature and scope of organic chemistry;

1.1. Highlights- History of Organic Chemistry

1.2. Bonding and Structure

1.2.1. The Nature of Organic Compounds

Organic chemistry is an empirical science whose developments have depended on millions

Fundamental to the structural theory are two central premises:

1.2.2. Electronic Structure and Bonding

1.3. The Formation of Chemical Bonds

1. gaining or losing enough electrons- an atom that gains an electron becomes a

1.3.1. The Ionic Bond

1.3.2. The Covalent Bond

● these atoms acquire completely filled valence shells by sharing electrons

A covalent bond is formed by sharing of electrons by two atoms. The formation of

1.4. Writing Correct Lewis Structures

There are two necessary features for a correct Lewis structure:

1) A carbon with four covalent bonds is neutral.

SAQ 1-1. Lewis Structure

Write a Lewis structure for each of the following:

4. H2CO3 10. NaOH

5. HNO3 11. CH2O

6. H2SO4 12. CH3OCH3

Recommended Online Reading

1) Lewis Symbols and Structures

1.5. Writing Molecular and Structural Formula

Lewis structures and ball-and-stick models of methane, ethane, and pentane.

A common method to simplify the drawings of larger molecules is to use a skeletal

SAQ 1-2. Drawing Skeletal Structures

Draw the skeletal structures for these two molecules:

Condensed formula Skeletal structure

The three classification of constitutional isomers are the following:

SAQ 1-3. Constitutional Isomers

1.7. Index of Hydrogen Deficiency (IHD)

Example: Write the possible structural formulas for:

Hence, the structural formula of C2H6O is

The structural formula of C3H6 is:

SAQ 1-4. Index of Hydrogen Deficiency

1.8. CHEMICAL BONDING THEORIES

Rule 1 The lowest-energy orbitals fill up first, according to the order 1s 2s 2p 3s 3p 4s

SAQ 1-5. Electron Configuration

1.8.1. VALENCE BOND THEORY (VBT)

1.8.2. Summary: Properties of Covalent Bond

3. Bond angle is the angle formed between two adjacent bonds.

F > O > Cl, N > Br > C, H

1.8.3. MOLECULAR ORBITAL THEORY (MOT)

Here are the key ideas of MOT:

Type of hybrid No. of s No. of p No. of p No. of hybrid

1.9.1. sp3 hybridization, methane as an example

1.9.2. sp2 hybridization, ethylene as an example

1.9.3. sp hybridization, acetylene as an example

Thus, in a Lewis structure, acetylene is composed of 2 triple-bond carbons: the bond

1.9.4. Examples of Overlapping Orbitals

1.9.5. Summary: Hybridization

Case 1: methane, CH4

Recommended Online Learning

1. Hybridization of Nitrogen, Oxygen, Phosphorus and Sulfur

SAQ 1-6. Hybridization

2. Arrange bonds A, B, and D according to:

1.11. Classification of Organic Compounds